vignettes/Converting_DICOM_to_NIfTI.Rmd
Converting_DICOM_to_NIfTI.RmdThe dcm2niir package creates simple wrapper for the ‘dcm2nii’ and ‘dcm2niix’ functions from Chris Rorden (https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage) for converting Digital Imaging and Communications in Medicine (DICOM) data to Neuroimaging Informatics Technology Initiative (NIfTI) formats.
For use in this vignette, we will download some mouse enhanced magnetic resonance image (MRI). In the case below, we are downloading a T1-weighted pre-contrast image. The dcm2niix software can handle individual DICOM images (1 dcm file per slice) or combined/3D DICOM images (1 dcm per volume). Below, the example dcm is an entire series/volume.
We will create a temporary directory and download the dcm file to that directory. We do this because dcm2niir::dcm2nii takes in a folder/directory as the main argument basedir.
library(utils)
# dcm_file = "ftp://medical.nema.org/medical/Dicom/DataSets/WG30/MGH/MR/MouseBrainSiemens15T_20150410/Converted/DICOM/mghmousetoenhancedmr_T1w_pre.dcm"
dcm_file = "http://johnmuschelli.com/dcm2niir/mghmousetoenhancedmr_T1w_pre.dcm"
tdir = tempfile()
dir.create(tdir)
destfile = tempfile(fileext = ".dcm", tmpdir = tdir)
ci = Sys.getenv("CI")
method = ifelse(ci == "", "auto", "curl")
dl = download.file(url = dcm_file, method = method,
destfile = destfile, mode = "wb")
dl == 0## [1] TRUE
file.exists(destfile)## [1] TRUEWe see a zero exit status and that the data exists. If this fails, you may not have ftp capabilities with R or your internet connection. Otherwise, this data may have moved, and please email the maintainer or submit an issue/bug report.
We load the library here and run the install_dcm2nii function. This downloads the binaries of the dcm2nii and dcm2niix software to use at the command line. This only needs to be run once after the installation of dcm2niir. Most functions should check this before running, so this step is not completely necessary, but allows you to check if dcm2niix is installed, and if not, it will install the binary.
## [1] TRUEThe main function is dcm2nii, and again the main argument is basedir. The argument copy_files indicates if the data from basedir should be copied to a temporary directory and dcm2nii will be run on that. This ensures nothing is done to the original data in case of a failure.
res = dcm2niir::dcm2nii(basedir = tdir)## #Copying Files## # Converting to nii## '/home/runner/work/_temp/Library/dcm2niir/dcm2niix_linux' -9 -v 1 -z y -f %p_%t_%s '/tmp/RtmpOHvMwY/file8e1b31a2ae24'## Warning in dcm2niir::dcm2nii(basedir = tdir): Result indicated an error! Please
## check results.
res## $result
## [1] 2
##
## $nii_before
## character(0)
##
## $nii_after
## character(0)
##
## $json_after
## character(0)
##
## $json_before
## character(0)
##
## $cmd
## [1] "'/home/runner/work/_temp/Library/dcm2niir/dcm2niix_linux' -9 -v 1 -z y -f %p_%t_%s '/tmp/RtmpOHvMwY/file8e1b31a2ae24'"The command line results from dcm2niix should be printed out along with the command.
We see the resulting list consisting of the result (exit status of dcm2niix - 0 means success), nii_before (filenames of NIfTI files in the directory before running), nii_after (filenames of NIfTI files in the directory before running, these are the converted ones), and the command passed to system (in the cmd slot).
There is a quick wrapper function called check_dcm2nii that takes this output. If there are multiple outputs for the same sequence, which may happen with variable slice thicknesses in the sequence (CT or MRI), which is interpolated, or gantry tilt (CT), then check_dcm2nii will try to choose the correct one. Otherwise, it returns the nii_after element. Either way, it returns a character vector:
checked = check_dcm2nii(res)
checked## character(0)
## attr(,"json_file")
## character(0)
file.exists(checked)## logical(0)Now this file can be read in using neurobase::readnii, ortho2::readNIfTI, RNifti::readNifti, or ANTsR::antsImageRead and be used as a 3D image.